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Wednesday, June 19, 2013

Extinction
events mark crises in the history of life, and recovery from these events
commonly is protracted. To better
understand the timing, nature, and controls of post-Permian biotic recovery, Galán-Abellán et al. document petrography,
whole-rock geochemistry, and isotopic analyses of early diagenetic aluminium-phosphate-sulphate
(APS) minerals in Early-Middle Triassic continental sandstones in the Iberian Ranges
(Iberian Peninsula). Sr and S isotopes
indicate mixed sources for these elements, derived from the dissolution of
pre-existing detrital minerals (phosphates, K-feldspar, clay minerals and
pyrite) and from marine and volcanic aerosols. The formation of APS minerals is
interpreted to be related to acid meteoric waters, which in turn reflect arid,
acidic conditions unfavorable to biotic recovery after the Permian–Triassic
biotic crisis. The study suggests that
analysis of APS minerals and Sr and S isotopes, coupled with sedimentologic and
stratigraphic analysis, can provide enhanced means to assess on
paleoenvironmental change and biotic recovery.

Friday, June 14, 2013

In this contribution, we enter somewhat murky waters….the posing of questions with ambiguous or uncertain answers, raised in the hope that they foster debate. Again, these are not the official views of SEPM.

Previous JSR Paper Clips posts (available here and here and here) have examined aspects of open access publishing. Careful readers may have noted several fundamental philosophical changes that have accompanied the shift towards open access, leading to new and continuing evolution of relationships among readers, authors, administrators, and even Congress.

As subscribers, readers traditionally have served the role of the customers and arbiters of quality—journals that published important papers would have a greater number of individual and library subscribers, and be well read. Journals with no readers would not be viable. With open access, if “all” papers are free and universally available, the publication system no longer reflects customer-based assessment of the quality of journals and the papers that they contain. Such an outcome would appear to require that pre-publication peer review fill this role of evaluating manuscripts, and in maintaining and rewarding quality papers and publications.

Yet, consider what some open access publishers tell us about peer review. Some open access publishers explicitly state that significance is not considered as a criterion for acceptance. Such a peer review model suggests “The peer review process does not judge the importance of the work, rather focuses on whether the work is done to high scientific and ethical standards and is appropriately described, and that the data support the conclusions.” An alternative open access model of “peer review” includes only “…a ‘binary’ accept or reject decision” that is based solely “on the basis of the validity of the research being reported, including the soundness of the research methods employed and the analysis undertaken to reach conclusions.”

Questions regarding the quality of the communication aside, leaving the evaluation of significance to the post-publication reader represents a fundamental shift from the approach of many journals. For example, a primary criterion for publishing a manuscript in JSR is that the manuscript clearly describes overarching question(s) of global relevance that the manuscript addresses. It is essential that papers in JSR “…..be agenda-setting, generic, and relevant to an international audience. The wider relevance must be explicit, in the title, abstract, introduction, and conclusions” (editorial May 2004). With the new “open access” review model, presumably an evaluation of significance is left to post-publication assessment.

Should post-publication commenting or “review” of some sort take the place of pre-publication peer review as a metric of scientific excellence and significance? What should be the form of “public” commentary—comments by whom? What are their credentials? Or, because chairs and deans will not take the time to read those comments (“The dean can’t read, but he can count”), will this lead to a situation in which the article-level or journal-level impact factors provide the sole metric of “quality” used for career advancement?

Traditionally, it has been regarded that “Publications are the currency of academia.” This statement is predicated on the notion that (at least with a traditional journal employing time-honored external pre-publication peer review) a publication reflects a well-written report on a quality study—the fact that it was published alone meant something. As is evident, however, this situation may not (or may) be the case today.

Beyond these changes, however, lies another basic question: Does the author “pays-for-publication” model create a fundamental conflict of interest? How does this model preclude the situation wherein “more money = more publications,” or, even more simply “money = publications,” especially given the lax standards of some OA publishers? Or, to quote Lord Cutler Beckett from Pirates of the Caribbean, are we now entering the situation wherein “Currency is the currency of the realm”? Does this advance science?

Perhaps it is more complex than that. For if this outcome is to be, consider how authors get some of their funding. Recent legislation working its way around Congress proposes new criteria for evaluation of National Science Foundation proposals that appear, to some, to “replace peer review.” (Having said that, the draft of the bill is somewhat ambiguous - do these replace, or extend beyond, the “intellectual merit” and “broader impacts” criteria already in place?) A draft of the proposed “High Quality Research Act” advocates that Congress should have some sort of oversight on “quality” science:

(a) “CERTIFICATION.—Prior to making an award of any contract or grant funding for a scientific research project, the Director of the National Science Foundation shall publish a statement on the public website of the Foundation that certifies that the research project—

(1) is in the interests of the United States to advance the national health, prosperity, or welfare, and to secure the national defense by promoting the progress of science;

(2) is the finest quality, is ground breaking, and answers questions or solves problems that are of utmost importance to society at large; and

(3) is not duplicative of other research projects being funded by the Foundation or other Federal science agencies.”

Along these lines, to flex their perceived authority, members of Congress actually requested access to “scientific/technical reviews and the Program Officer’s Review Analysis” of specific, individual NSF grants. Does Congress now advocate that it provide oversight beyond (or replace?) the peer-review process? Is this level of oversight appropriate? Should Congress proactively “call the piper’s tune?”

Since at least the 17th century, the scientific community, through the work of scholarly societies, has served an important role in the development (e.g., conferences where ideas are discussed in person), organization (into peer groups, facilitating specialized, topical journals), and validation (through peer review) of quality science communication—perhaps playing the most important role in science, other than that of the scientists themselves. The first few posts of this series (available here and here) explored some of the issues that may arise for scholarly societies as a result of mandated open access. In this new world, with a) no subscriptions, b) limited (no?) pre-publication peer assessment of significance (but with congressional oversight?), and/or c) authors who can pay to publish almost anything, what is the role of scholarly societies in this publishing evolution/revolution? Are the days (indeed … the centuries!) where their journals stand as hallmarks of quality publications soon to be (or already) over? Will there be publications and “publications”? What is the appropriate relationship among readers, authors, and societies? Is there only one relationship? If not, what are the appropriate metrics for excellent scholarly papers and publications, and how do societies best serve to ensure quality?

Or, at an even larger scale, what is the appropriate place for scholarly societies in this politically mandated changing landscape?

One goal of societies is keeping the community abreast of changes in the science world. We at JSR Paper Clips hope that our series has helped inform you about some of the dynamic publication world (as readers, authors, and interested parties), and motivate you to dig deeper, for these changes will impact all of us. Now, however, until further developments, we continue with our regular programming….

This post represents one of a series in JSR Paper Clips. These posts are available here:

Thursday, June 13, 2013

Since the initial 1665 publication of Philosophical Transactions of the Royal Society of London, followed by publication of the first fully peer-reviewed journal,Medical Essays and Observations, by Royal Society of Edinburgh, scholarly societies have played an important role in ensuring the validity, rigor, and accuracy of scientific publications. With paper publications came a high printing cost; one which societies offset by offering subscriptions. This high cost of the printed page provided a sort of “filter,” by which only the highest quality manuscripts made it into print.

Recent advances in e-publishing and internet distribution have changed the scholarly publication landscape forever, with the possibility of low-cost publishing, including “unlimited” online distribution of scientific publications. This step, coupled with the recent push towards open access, has enticed many entrepreneurs to develop purely open access journals. Many of these journals use an author-pays model, in which authors pay to publish their materials, which are then distributed electronically for “free.” Authors (or is it funding agencies?) become the publisher’s customers. In this financial model, publishers are faced with a pressure to publish papers—the more papers the better, often with limited editorial or quality oversight. Conversely, only those with funding can publish. On the other hand, the publishers could use some oversight. Consider the American Journal of Earth and Planetary Science author guidelines, which state “publication charge are need for article maintenance, long times keeps for archives. All reader cans read article absolutely free and readers can print, download and copy. (Before publication author need to pay publication fee and after made payment author need to send payment made receipt to publisher.)” [sic]. Perhaps not surprisingly, with many of these publication outlets, quality and integrity issues have arisen. For example, consider the penetrating and life-altering paper, “The Subtotal Button for Summarizing Data in an Excel Database,” published in 2011 by the Journal of Knowledge Management, Economics and Information Technology, or perhaps the more recent (and relevant?) “What is Good e-Learning?” Is this the future of scientific publishing???

Unchecked implementation of aspects of open access can be incongruous with the goal of excellence in scientific communication. Beyond these issues of quality with some open access titles, unfortunate situations can arise, even if a quality paper is published.

Open access advocates commonly seek to use a Creative Commons license. A large open access publisher, Public Library of Science, or PLoS, uses a version of the license that permits “anyone to download, reuse, reprint, modify, distribute, and/or copy the content as long as the original authors and source are cited. No permission is required from the authors or the publishers.” [emphasis in original] This license means that anyone, anywhere, can freely re-post or re-publish any or all of the original work, as long as the original is cited. [This license is the same required by the Research Council of the United Kingdom (RCUK).] Unscrupulous publishers appear to take advantage of this license, as evidenced by two recent accusations of plagiarism in which entire open access PLoS papers were re-published in sketchy journals. Interestingly, these shady journals even had acknowledged editorial board members who were not even aware that they were listed.

Even more egregious are publishers such as Open Research Network (ORN), a new publisher with 86 journal titles. Their website trumpets that they are “a purpose-driven and open-source knowledge dissemination organization” with the mission of “sharing academic knowledge through Publishing the most exciting researches with respect to the subjects of our Journals and providing a rapid turn-around time possible." Some titles are so new that they do not have an editorial board; others appear to have been generated by an innovative method: ORN copied them, word for word, from another publisher!!! Unfortunately, this publisher is not an outlier; see the blog by Jeffrey Beall, a research librarian at University of Colorado-Denver, for continuing insights. These, and other predatory open access publishers clearly act only to lower the bar in scientific publishing.

Perhaps the moral of this study is that authors of papers with CC-BY licenses should be aware that their work may re-appear in other places—and authors should consider if “free access” should be synonymous with “free to use as you like.” Whatever the case, science is not furthered via a free-for-all.

Scholarly societies serve to aggregate and organize the community, and are dedicated to excellence in publications. Unlike for-profit publishers whose subscription profits go to shareholders, or author-pays open access journals that have pressure to publish more papers to profit, JSR serves the community by vettinghigh-quality contributions to sedimentary geology and paleontology. The long (and continuing) publication history of influential papers and high (and rising) citation indices in JSR (and other SEPM publications) are, and will continue to be, a manifestation of this focus.

This
post represents one of a series in JSR
Paper Clips. These posts are
available here:

Wednesday, June 12, 2013

Who doesn’t like a free lunch? The last Paper Clips post discussed the expanding federal mandates that require free online public access to publications sponsored by large federal research programs. The vision of free online public access to journal publications will aid in widespread dissemination, including the general public, and it does not discriminate against those who would otherwise be unable to afford subscriptions. And, taxpayers have “already paid.”

Broadly consistent with the goal of expanding knowledge, the purpose of SEPM (as articulated on its website) indicates dedication “…to the dissemination of scientific information on sedimentology, stratigraphy, paleontology, environmental sciences, marine geology, hydrogeology, and many additional related specialties.”

And like a free lunch, who wouldn’t like their journal articles widely and freely distributed!? So this mandate is a good thing, right? Maybe. Or, maybe not. There is a cost to publishing. At one end of the spectrum, Natureestimates costs of $30,000–40,000/published article (in part related to the high rejection rate, and the inclusion of editorials, commentary, and related news stories). Most publishers, especially scholarly society publishers, carry less overhead, but still incur real costs, as discussed in the last post.

As Robert Heinlein put it “There ain’t no such thing as a free lunch.” Someone has to pay…and the same is true for the services provided by notionally “free” journals or e-books. Taxpayers have paid for the research, but will they pay for the cost of publishing the results of the research? Will funding agencies cover the production costs of open access articles that many journals charge for using an open access option? What about those authors that do not have any funding sources, but want (or need) their article to be OA? If so, who pays then? Will other contributors effectively subsidize these authors?

As of early June, 2013, policies for NSF and DOE have not been finalized, so for sedimentary geologists, the frank answer is: “We don’t know.” But there are clues. For example, The Research Council’s UK policy is that funding for open access “will be available through a block grant awarded directly to research organisations.” It was unclear (to this blogger) how these funds are to be administered among and within organizations, however. What kind of author competition might exist to get these funds? Will scientists or institutions be penalized for being too productive and exceeding their “publication allowance”? Back in the U.S., the new mandate explicitly requires that agencies respond with a plan that contains “identification of resources within the existing agency budget to implement the plan” [emphasis added]. How have other programs responded? NIH policy states that it will reimburse publication costs, unless the grant does not have sufficient funds, at which point grantees are advised to “consult with your institutional official for advice and options.”

What then are institutional policies? A leader in the drive for open access, the Massachusetts Institute of Technology has a clear “step-by-step” policy. In it, they note that the NIH open access policy (remember—we don’t know the NSF and DOE policy yet) might include costs for publishing in an open access journal that has article processing charges or a traditional subscription-based journal that has authors select an “open access option.” Their guide suggests that authors realize three points:

·“NIH will allow PIs to pay open access publication costs from grant funds, though NIH is not budgeting additional funds for this purpose.

·MIT will not absorb these costs.

·Authors should not feel obliged to pay a traditional subscription journal an additional open access fee. You may opt to submit the MIT amendment and request that the publisher comply, without participating in a paid open access program.”

Read those again. NIH has no additional funds…the institution will not pay for them…and, neither should authors.

OK, so who pays? Who else is left, but subscribers (readers and libraries) or publishers? Yet, if articles are available online for free (“gold” open access), why would any reasonable person (or a librarian under budget pressure) pay to be a subscriber? Along these lines, a 2006 survey of librarians found that “if two-fifths of a journal’s articles became free within 12 months, 44% said they would cancel their subscriptions.” (Kaiser 2010). More recent reports reveal comparable results.

So then the answer—if authors refuse to pay or readers cancel subscriptions, or both—is that scholarly publishers seem to be left to cover expenses. A recent editorial by The Ecological Society of America suggested that they “…could suffer potentially severe consequences from laws that would force it to make significant changes to its business model within a limited time frame. …the future of ESA as currently operated would be very much in question.” The same is true for many scholarly societies.

Open access is here; that train has left the station. The August release of federal agency policies and implementation plans will be enlightening, and hopefully will remove some ambiguity and uncertainty. The SEPM Council is now developing an official open access policy and working to plan a path forward. Beyond these steps, we encourage JSR Paper Clips readers to learn more about open access, and the implications and the opportunities for both authors and scholarly societies.

This
post represents one of a series in JSR
Paper Clips. These posts are
available here:

Monday, June 10, 2013

Scholarly and scientific publishing is rapidly changing.With the goal of helping to keep JSR Paper
Clips readers, Journal of Sedimentary Research authors, and the community of sedimentary geologists and paleontologists
informed, this post is the first of a series that explores continuing
developments in this area.The posts are
provided not as official views or policies of SEPM, but rather as my perspectives
as an editor, author, and faculty member at an institution that seeks to be a
leader in the open access movement.

Recently (February 2013), the White House Office of Science
and Technology Policy (OSTP) issued guidelines for “Increasing Access to the Results of Federally Funded
Scientific Research” to heads of federal agencies. Dr.
John Holdren, director of OSTP, summarized the basic idea as “… scientific
research supported by the Federal Government spurs scientific breakthroughs and
economic advances when research results are made available to
innovators…. Moreover, this research was funded by taxpayer dollars. Americans
should have easy access to the results of research they help support” [emphasis
added].To accomplish these goals, the
new edict directs Federal agencies with “more than $100 million in research
and development expenditures to develop plans to make the results of
federally-funded research publicly available free of charge within 12 months
after original publication.” U.S. government agencies that fall
into this category (including NSF, DOE, NASA, USGS, and other sedimentary
geology-supporting agencies) have until August to formulate their policies and
implementation plans.

Such motivations and plans are not new; and to most, “results
of research” means publications. The U.S. National Institutes of Health (NIH)
have had such a policy for years, as has the Research Councils of the UK, whose
requirements,
including open access upon publication, became active in April 2013. What
will actually happen for sedimentary geologists in the U.S. is unclear, as each
agency develops its own plans, and as some of the guidelines are nebulous, and various groups jockey for influence. For example,
although the OSTP guidelines call for a “twelve-month post-publication
embargo period as a guideline” [emphasis added], a new bill in the US House requires “free online public access…not later than 6
months after publication.”

Free, unrestricted access to scientific publications –—including scholarly society journals—while obviously every reader’s (and
authors?) wish, has implications. In journal production, scholarly
societies incur costs related to using the e-portals for manuscript management,
staff to assist authors and editors to maintain timely flow of manuscripts,
copy editing, and final formatting into a journal paper, DOI assignment and
registration, file checking and uploading, online support for access, not to
mention web hosting and archiving, etc.—the list is long. As noted by the
Feds, scholarly publishers “provide valuable services, including the
coordination of peer review, that are essential for ensuring the high quality
and integrity of many scholarly publications. It is critical that these
services continue to be made available.”Beyond these considerations, many non-profit society publishers rely on
some amount of positive revenue from publications to allow them to subsidize
other activities (e.g., short courses, field trips) that cannot easily pay
their own costs, yet which are important to fulfill their science mission.

The next post will explore this concern more,
but it appears that open access could cause fundamental modifications to the
means by which some scholarly societies serve the community.

This
post represents one of a series in JSR
Paper Clips. These posts are
available here: